Molecular Cell Biology 5068 In class Exam 1 October 2, Please print your name: Instructions:

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1 Molecular Cell Biology 5068 In class Exam 1 October 2, 2012 Exam Number: Please print your name: Instructions: Please write only on these pages, in the spaces allotted and not on the back. Write your number on each page (not your name), so that we can split them up and grade them anonymously. There are a total of 6 pages including this cover page. You may not use any books or notes, and no electronic aids, including calculators. Answer only in the space provided; short, concise answers are preferred and will be rewarded. Please be as neat as possible. When you are finished, turn this in to the TA and pick up the take-home portion.

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3 MCB 5068 Exam 1 October 2, 2012 Exam Number: In Class Questions for Dr. Cooper s lectures. 1. True or False (correct the statement if false): Enthalpy is the primary driving force for self-assembly of protein-based polymers. (2 pts) 2. True or False (correct the statement if false):a competitive inhibitor binds the enzyme and the enzymesubstrate complex. (2 pts) 3. With respect to actin filaments or microtubules, what does the term treadmilling mean? (3 pts) 4. List 3 mechanisms by which cytoskeleton polymer assembly is regulated. (3 pts) 5. Describe the steps involved in myosin movement along actin. (5 pts) -1-

4 6. a) State the names of the extensions found at the leading edge of a motile cell, b) Describe the nature of the actin filament network found in each of the extensions, and c) State the names of the actin binding proteins that are necessary for the formation of the networks in each case. (5 pts) 7. Name two cellular processes in which microtubule motors, kinesin and dynein, play important roles. Describe the role of each of the motors in each of the processes. Be as specific as possible. (4 pts) 8. How are intermediate filaments assembled? (3 pts) How can incorporation of a single mutant subunit weaken the entire filament network? (2 pts) -2-

5 In Class Questions for Dr. Mueckler s lectures. Exam Number: 1. List 2 functions of biological membranes. (2 points) - 2. What do we mean when we say that a molecule is amphipathic? (2 points) 3. True or False (correct the statement if false): All membrane helices present in multipass proteins are amphipathic. (2 points) 4. Name 2 energetically favorable structures that lipids can form in aqueous solution and draw them (2 points) 5. List the 4 types of phospholipid movements that occur within bilayers. Which type of movement is the least energetically favorable? (4 points) 6. True or False (correct the statement if false): Phosphoglyceride biosynthesis occurs in a sequential manner with individual steps occurring alternately at the luminal or cytoplasmic face of the ER. (2 points) -3-

6 7. Differentiate between the activity of scramblase and flippase enzymes. (2 points) 8. Name 2 intracellular signaling molecules produced upon activation of phospholipase C in a membrane containing phosphatidyl inositol triphosphate. (2 points) 9. With the aid of a diagram, outline the steps in the signal-mediated targeting of proteins to the ER. In the diagram, be sure to show the SRP, SRP receptor, and mechanism for closing and opening of the translocon. (4 points) 10. True or False (correct the statement if false): Secretory signal sequences are always located at the N- terminus and share sequence similarity among different preproteins. (2 points) -4-

7 Exam Number: 11. Membrane protein topologies are classified into how many basic types? Draw and name an example of a membrane protein with single-pass topology. Be sure to show the location of the N- and C-terminus of the protein with respect to the cytosolic and luminal (or extracellular) face of the membrane. (1 point for providing the number of types) (3 points for showing one example) 12. What is the function of protein disulfide isomerase (PDI) and where is it located in the cell? (2 points) 13. True or False (correct the statement if false): Most mitochondrial proteins are encoded in the nuclear DNA. (2 points) 14. Import into the mitochondrial matrix requires passage through 2 separate translocons named and. The proteins traverse in a (choose between folded or unfolded) state. (3 points) 15. Describe targeting of proteins to the outer mitochondrial membrane via the SAM protein complex. (4 points) -5-

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9 Hanson Lecture 1 Endoplasmic Reticulum: quality control, processing, and exit Exam Number: 1. A terminally misfolded protein in the endoplasmic reticulum (ER) can be identified by which of the following features? (2 points) A. The presence of multiple ubiquitin molecules attached to the protein B. The presence of the protein in a complex with Calnexin/Calreticulin C. The absence of glucose molecules in the N-linked oligosaccharide D. The absence of mannose molecules in the N-linked oligosaccharide 2. Briefly explain how the Unfolded Protein Response (UPR) is regulated by the action of BiP, Ire1, and Hac1. (4 points) 3. True or False (correct the statement if false): Vesicle coat proteins are necessary to maintain vesicle structural integrity and allow fusion into the target membrane. (2 points) 4. Name two cellular strategies for dealing with ER stress induced by the Unfolded Protein Response (UPR)? (2 points) 5. You design an experiment in which you transfect cells with GFP-labeled temperature-sensitive VSVG protein. You are observing the cells at the non-permissive temperature and see diffuse reticular fluorescence throughout the cell. When the cell is then moved to the permissive temperature, you see rapid accumulation of the GFP in the perinuclear region. Describe the cellular/molecular process underlying this observation. (4 points) -7-

10 Hanson Lecture 2 Secretory Pathway, Membrane Fusion 6. Endoglycosidase D can be used to determine if a protein is within the ER or cis-golgi due to which of the following modifications of secreted proteins as they pass through the Golgi apparatus? (2 points) 7. You identify a specific and highly efficacious inhibitor of NSF (NEM-sensitive factor). If you apply the inhibitor and simultaneously stimulate a neuron, what changes in neurotransmitter release would you expect in the short run and long run? Why? (4 points) 8. Botulinum toxin and tetanus toxin both act on the same molecular targets but produce drastically different symptoms. What is the class of proteins that is targeted by these toxins and why are the effects different? (3 points) Hanson Lecture 3 Lysosomes and Endocytic Pathways 9. True or False (correct statement if false): In both clathrin-mediated and caveolar endocytosis, dissociation of the coat proteins from the vesicle membrane is required for cargo release. (2 points) -8-

11 Exam Number: 10. You identify a novel mutation in the endosomal H + pump responsible for acidifying endosomal compartments that inactivates it. How would you expect this mutation to affect cellular levels of cholesterol derived from LDL breakdown? How might this affect LDL Receptor recycling? Why? (4 points) 11. Activating EGF-Receptor (EGFR) mutations are known to contribute to cancer development and progression. Why might mutations in ESCRT proteins mimic activating mutations in the EGFR? Explain. (4 points) 12. You are working with a cell line that requires Fe 3+ uptake via the transferrin receptor (Tf-R) for propagation. If you treat these cells with RNAi targeted to Rab11, which of the following changes in Tf-R localization would you expect? (2 points) A. Decreased concentration of the Tf-R in early endosomes B. Decreased concentration of Tf-R in late endosomes C. Decreased concentration of Tf-R in the mitochondrial membrane D. Decreased concentration of Tf-R in the plasma membrane E. Increased concentration of Tf-R in the nuclear membrane -9-